\hypertarget{classpipe__struct}{
\section{pipe\_\-struct Class Reference}
\label{classpipe__struct}\index{pipe\_\-struct@{pipe\_\-struct}}
}


Either builds co-\/orthologs or builds the strings for the result file.  




{\ttfamily \#include $<$pipe\_\-struct.h$>$}



Collaboration diagram for pipe\_\-struct:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[height=600pt]{classpipe__struct__coll__graph}
\end{center}
\end{figure}
\subsection*{Public Member Functions}
\begin{DoxyCompactItemize}
\item 
\hypertarget{classpipe__struct_a2e4bd1642de55f4731dc37bafedd4d03}{
void \hyperlink{classpipe__struct_a2e4bd1642de55f4731dc37bafedd4d03}{getFromBufferToStruct} (const uint taxon\_\-length, uint max\_\-buffer\_\-size, const bool only\_\-inparalogs)}
\label{classpipe__struct_a2e4bd1642de55f4731dc37bafedd4d03}

\begin{DoxyCompactList}\small\item\em Opens a buffer and dumps it to memory if the space for it is allocated. \end{DoxyCompactList}\item 
\hypertarget{classpipe__struct_a3671204dcf9fc367a8d3fa257168e8c0}{
void \hyperlink{classpipe__struct_a3671204dcf9fc367a8d3fa257168e8c0}{finalize\_\-memory} (const uint taxon\_\-length)}
\label{classpipe__struct_a3671204dcf9fc367a8d3fa257168e8c0}

\begin{DoxyCompactList}\small\item\em Clears the memory allocated for this thread. \end{DoxyCompactList}\item 
\hypertarget{classpipe__struct_aed3e03bc6bc544e326efac9a07a24025}{
void $\ast$ \hyperlink{classpipe__struct_aed3e03bc6bc544e326efac9a07a24025}{operator()} (void $\ast$item)}
\label{classpipe__struct_aed3e03bc6bc544e326efac9a07a24025}

\begin{DoxyCompactList}\small\item\em The method of parallisation. \end{DoxyCompactList}\item 
\hypertarget{classpipe__struct_ae9dc6e2a83cb63bcb5ef42be0ae3a2ca}{
void \hyperlink{classpipe__struct_ae9dc6e2a83cb63bcb5ef42be0ae3a2ca}{free\_\-mem} ()}
\label{classpipe__struct_ae9dc6e2a83cb63bcb5ef42be0ae3a2ca}

\begin{DoxyCompactList}\small\item\em De-\/allocates the memory reserved for this object. \end{DoxyCompactList}\item 
\hyperlink{classpipe__struct_aac0130667428da2ba6042e6ff4a34961}{pipe\_\-struct} (uint \_\-nthread, uint \_\-size\_\-prot, uint taxon\_\-length, pipe\_\-t type, bool \_\-USE\_\-EVERYREL\_\-AS\_\-ARRNORM\_\-BASIS, norm\_\-t $\ast$$\ast$normArr, log\_\-builder\_\-t $\ast$\_\-log, bool \_\-MODE\_\-PAIRWISE\_\-OUTPUT, bool \_\-MODE\_\-INTEGER\_\-OUTPUT, bool \_\-DIVIDE\_\-BY\_\-NORMALIZATION\_\-VALUE\_\-FOR\_\-ABC\_\-FORMAT, bool \_\-DIVIDE\_\-BY\_\-NORMALIZATION\_\-VALUE\_\-FOR\_\-MCL\_\-FORMAT, id\_\-simil\_\-list \&\_\-listOrtho, taxa\_\-t $\ast$\_\-listTaxa, stack\_\-rel $\ast$\&\_\-stackRel, list\_\-file\_\-struct\_\-t $\ast$\&\_\-listStructData, list\_\-file\_\-parse\_\-t $\ast$\&\_\-listParseData, float \_\-max\_\-input\_\-value, bool \_\-MODE\_\-PAIRWISE\_\-OUTPUT\_\-ABC, bool \_\-MODE\_\-PAIRWISE\_\-OUTPUT\_\-MCL, bool \_\-PRINT\_\-IN\_\-ABC\_\-FORMAT, bool \_\-PRINT\_\-IN\_\-MCL\_\-FORMAT, bool \_\-SORT\_\-ABC\_\-DATA, bool \_\-PRINT\_\-NORMALIXATION\_\-BASIS, bool \_\-DEBUG\_\-NORM)
\begin{DoxyCompactList}\small\item\em Constructor for the class. \end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
Either builds co-\/orthologs or builds the strings for the result file. 

\begin{DoxyReturn}{Returns}
A 'bucket\_\-norm object. 
\end{DoxyReturn}
\begin{DoxyAuthor}{Author}
Ole Kristian Ekseth (oekseth) 
\end{DoxyAuthor}
\begin{DoxyDate}{Date}
21.12.2010 by oekseth (initial) 

16.09.2011 by oekseth (asserts) 

24.12.2011 by oekseth (removed calls to 'extern' variables to ease the inclusion of thisclass as a libary) 

25.12.2011 by oekseth (cleanup). 
\end{DoxyDate}


\subsection{Constructor \& Destructor Documentation}
\hypertarget{classpipe__struct_aac0130667428da2ba6042e6ff4a34961}{
\index{pipe\_\-struct@{pipe\_\-struct}!pipe\_\-struct@{pipe\_\-struct}}
\index{pipe\_\-struct@{pipe\_\-struct}!pipe_struct@{pipe\_\-struct}}
\subsubsection[{pipe\_\-struct}]{\setlength{\rightskip}{0pt plus 5cm}pipe\_\-struct::pipe\_\-struct (
\begin{DoxyParamCaption}
\item[{uint}]{\_\-nthread, }
\item[{uint}]{\_\-size\_\-prot, }
\item[{uint}]{taxon\_\-length, }
\item[{pipe\_\-t}]{type, }
\item[{bool}]{\_\-USE\_\-EVERYREL\_\-AS\_\-ARRNORM\_\-BASIS, }
\item[{norm\_\-t $\ast$$\ast$}]{normArr, }
\item[{log\_\-builder\_\-t $\ast$}]{\_\-log, }
\item[{bool}]{\_\-MODE\_\-PAIRWISE\_\-OUTPUT, }
\item[{bool}]{\_\-MODE\_\-INTEGER\_\-OUTPUT, }
\item[{bool}]{\_\-DIVIDE\_\-BY\_\-NORMALIZATION\_\-VALUE\_\-FOR\_\-ABC\_\-FORMAT, }
\item[{bool}]{\_\-DIVIDE\_\-BY\_\-NORMALIZATION\_\-VALUE\_\-FOR\_\-MCL\_\-FORMAT, }
\item[{id\_\-simil\_\-list \&}]{\_\-listOrtho, }
\item[{taxa\_\-t $\ast$}]{\_\-listTaxa, }
\item[{stack\_\-rel $\ast$\&}]{\_\-stackRel, }
\item[{list\_\-file\_\-struct\_\-t $\ast$\&}]{\_\-listStructData, }
\item[{list\_\-file\_\-parse\_\-t $\ast$\&}]{\_\-listParseData, }
\item[{float}]{\_\-max\_\-input\_\-value, }
\item[{bool}]{\_\-MODE\_\-PAIRWISE\_\-OUTPUT\_\-ABC, }
\item[{bool}]{\_\-MODE\_\-PAIRWISE\_\-OUTPUT\_\-MCL, }
\item[{bool}]{\_\-PRINT\_\-IN\_\-ABC\_\-FORMAT, }
\item[{bool}]{\_\-PRINT\_\-IN\_\-MCL\_\-FORMAT, }
\item[{bool}]{\_\-SORT\_\-ABC\_\-DATA, }
\item[{bool}]{\_\-PRINT\_\-NORMALIXATION\_\-BASIS, }
\item[{bool}]{\_\-DEBUG\_\-NORM}
\end{DoxyParamCaption}
)}}
\label{classpipe__struct_aac0130667428da2ba6042e6ff4a34961}


Constructor for the class. 

\begin{DoxyRemark}{Remarks}
Operation decided when setting the 'PIPE\_\-TYPE' variabel (PIPE\_\-TYPE == DUMP): Writes the data to a matrix, for further processing by another program (PIPE\_\-TYPE == INPA\_\-ORTH) Creates inparalogs based upon orthologs. (PIPE\_\-TYPE == INPA\_\-INPA) Creates inparalogs based upon orthologs' inparalogs. 
\end{DoxyRemark}


The documentation for this class was generated from the following file:\begin{DoxyCompactItemize}
\item 
\hyperlink{pipe__struct_8h}{pipe\_\-struct.h}\end{DoxyCompactItemize}
